How to Fix Error in snpeff

Question

[misbahabas]

Asslamu Alikum

I am using snpeff to annotate vcf files, When I run command it gives some errors and warnings

java -Xmx4g -jar snpEff.jar CanFam3.1.75 -v /media/misbah/dccc4c9e-df84-4f29-bd64-e6f88cf7dbce/DQ1.g.vcf > DQ1.ann.vcf

It give error at the end of completion

ERRORS: Some errors were detected
Error type  Number of errors
ERROR_CHROMOSOME_NOT_FOUND  285197

WARNINGS: Some warning were detected
Warning type    Number of warnings
INFO_REALIGN_3_PRIME    6443
WARNING_TRANSCRIPT_INCOMPLETE   277
WARNING_TRANSCRIPT_NO_START_CODON   678825
WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME  943
WARNING_TRANSCRIPT_NO_STOP_CODON    499400
WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME   346

Is it effect on the results? I don't know how to fix it.

Please tell me about it

Thanks

[lakhujanivijay]

It says, ERROR_CHROMOSOME_NOT_FOUND 285197

Can you please check your vcf for this?

[Matteo Schiavinato]

What do you get if you do:

bcftools view -H yourvariantsfile.vcf | awk '$1=="285197"'

And if you do:

bcftools view -h yourvariantsfile.vcf | awk '$1=="285197"'

(not that in the first case I am asking to show only the variants called, in the second case only the header)

[misbahabas]

when i run first command It give result like that

[bcf_sync] incorrect number of fields (0 != 5) at 0:0

and in second case are also same

[bcf_sync] incorrect number of fields (0 != 5) at 0:0

[Matteo Schiavinato]

Then the header of your file is corrupted. How did you generate it?

[supriyaslsuman97]

When i had run both the commands Nothing was seen in my case.

Answer 1

[Razi]

Hi,

I have the same issue. Would you please help me to solve this?

I ran this command:

java -Xmx4g -jar snpEff.jar -c snpEff.config -v BF BF.vcf.gz > BF.ann.vcf

And Got this error:

"RRORS: Some errors were detected Error type: ERROR_CHROMOSOME_NOT_FOUND Number of errors: 8419432"

I check these: bcftools view -H BF.vcf.gz | awk '$1=="8419432"' bcftools view -h BF.vcf.gz | awk '$1=="8419432"'

and there was no answer!

Would you please help me? Thanks!

[Pierre Lindenbaum]

Number of errors: 8419432"

it's a number of errors. Why on earth would you find the number of errors in the column 1 of a VCF ?!!

[Razi]

I don't know?! So what is your suggestion? Do you think it can be because of gff file?

Thanks!

[Razi]

how you find it is from column 1?

[Razi]

I found the solution. Please look at this link:(https://pcingola.github.io/SnpEff/se_faq/#error_chromosome_not_found-details)